There exist 17 studies that have investigated the growth forms of Acropora cervicornis at the genotype level which have been incorporated into our database. These studies began with Diego Lirman who analyzed genotype-specific differences in annual proportionate growth (termed productivity in Lirman et al. 2014) across genotypes within Diego’s Biscayne National Park nurseries and his work in the Dominican Republic. Katie Lohr built upon this and analyzed 10 genotypes for differences in total linear extension and calcification rate over a 13 month study of CRF genotypes (Lohr and Patterson 2017). At the same time, Ford Drury analyzed the genotype niches in a genotype by environment study (Dury, Manzello, Lirman 2017). Other studies did not solely focus on differences among genotypes but their data analyzing growth under OA, temperature stress, or a combination of the two shed light on genotype-specific patterns. There has consistently been genotypic patterns of growth throughout all of these studies. Through the connection of each individual dataset, we can elucidate new, overarching genotype-specific patterns of growth. Below is a table summarizing the aforementioned and complementary studies that have analyzed growth of genotyped A. cervicornis. The remaining tables delve into the combined data of all these studies to begin to draw patterns.
| trait | unit | method | mean | sd | min | max | n | datasets | genotypes |
|---|---|---|---|---|---|---|---|---|---|
| 6-month colony volumetric growth | proportionate growth | 3D photogrammetry | 2.5333658 | 4.5160081 | 0.0377524 | 60.281553 | 293 | 3 | 17 |
| 6-month interstitial space growth | proportionate growth | 3D photogrammetry | 6.3103033 | 5.5360624 | 0.0692467 | 35.728773 | 135 | 1 | 10 |
| 6-month linear growth | proportionate growth | ruler | 1.6449644 | 1.4264161 | 0.0133041 | 16.524444 | 2686 | 10 | 120 |
| annual colony volumetric growth | annual proportionate growth | 3D photogrammetry | 6.5244687 | 8.1461205 | 0.3835854 | 63.974185 | 170 | 3 | 18 |
| annual interstitial space growth | annual proportionate growth | 3D photogrammetry | 22.6691608 | 23.9115484 | 1.4555964 | 216.829571 | 123 | 1 | 10 |
| annual linear growth | annual proportionate growth | ruler | 6.6611193 | 5.8815492 | 0.0405556 | 59.211111 | 1583 | 9 | 81 |
| colony volumetric SGR | % change day^-1 | 3D photogrammetry | 0.5092050 | 0.1972331 | 0.0883920 | 1.376506 | 317 | 4 | 23 |
| daily calcification | mg day^-1 | buoyant weight | 71.5996332 | 96.9861159 | 3.9540230 | 497.308997 | 266 | 5 | 32 |
| dark calcification | µmol cm^-2 h^-1 | alkalinity anomaly | 0.6967946 | 0.2713945 | 0.0180000 | 1.594000 | 56 | 1 | 12 |
| interstitial space SGR | % change day^-1 | 3D photogrammetry | 0.7736615 | 0.2390515 | 0.2423776 | 1.520514 | 136 | 1 | 10 |
| light calcification | µmol cm^-2 h^-1 | alkalinity anomaly | 0.8475254 | 0.2766803 | 0.3110000 | 1.594000 | 59 | 1 | 12 |
| mass normalized daily calcification | mg day^-1 g^-1 | buoyant weight | 27.2406909 | 41.4262869 | 0.3450656 | 191.199153 | 244 | 4 | 27 |
| SA normalized daily calcification | mg day^-1 cm^-2 | buoyant weight | 1.2370585 | 0.3665081 | 0.5407155 | 2.884992 | 105 | 2 | 13 |
| specific growth rate | % change day^-1 | ruler | 0.5105088 | 0.2186303 | 0.0062386 | 1.597730 | 2867 | 11 | 122 |
| genotype | specific growth rate | 6-month linear growth | annual linear growth | colony volumetric SGR | annual colony volumetric growth | 6-month colony volumetric growth | 6-month interstitial space growth | annual interstitial space growth | interstitial space SGR | daily calcification | mass normalized daily calcification | SA normalized daily calcification | dark calcification | light calcification |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ML41 | 0.40 | 1.32 | 3.96 | 0.45 | 4.09 | 2.31 | 6.34 | 16.72 | 0.80 | 22.02 | 1.85 | 1.13 | 0.91 | 0.82 |
| ML7 | 0.36 | 0.99 | 3.48 | 0.53 | 7.25 | 1.88 | 6.93 | 32.14 | 0.86 | 34.82 | 2.51 | 1.25 | 0.74 | 0.88 |
| ML62 | 0.56 | 2.10 | 4.88 | 0.49 | 6.67 | 1.73 | 7.52 | 30.94 | 0.83 | 9.57 | 1.90 | 0.98 | 0.48 | 0.84 |
| ML50 | 0.51 | 1.86 | 5.62 | 0.43 | 6.05 | 1.55 | 6.68 | 30.46 | 0.74 | 10.98 | 2.34 | 1.25 | 0.84 | 0.73 |
| ML31 | 0.43 | 1.86 | 4.40 | 0.35 | 2.73 | 1.54 | 6.41 | 16.42 | 0.71 | 20.17 | 2.05 | 1.13 | 0.92 | 0.87 |
| ML3 | 0.43 | 1.70 | 4.55 | 0.44 | 5.13 | 1.51 | 5.77 | 19.12 | 0.71 | 9.66 | 2.02 | 1.09 | 0.75 | 0.71 |
| ML44 | 0.43 | 1.15 | 4.51 | 0.50 | 6.35 | 1.31 | 4.37 | 17.44 | 0.70 | 21.41 | 2.10 | 1.20 | 0.65 | 0.99 |
| ML1 | 0.45 | 1.50 | 3.80 | 0.43 | 4.63 | 1.30 | 3.98 | 17.74 | 0.76 | 15.87 | 1.32 | 1.36 | 0.64 | 0.67 |
| ML13 | 0.46 | 1.29 | 3.42 | 0.35 | 2.94 | 1.13 | 6.73 | 19.49 | 0.78 | 7.12 | 1.54 | 0.92 | 0.65 | 0.87 |
| ML36 | 0.39 | 0.95 | 3.66 | 0.49 | 5.82 | 1.70 | 7.94 | 23.95 | 0.85 | - | - | - | - | - |
| M6 | 0.57 | 1.72 | - | 0.54 | 11.98 | 5.30 | - | - | - | 12.77 | 0.89 | - | - | - |
| U41 | 0.70 | 5.52 | 13.29 | 0.54 | 5.30 | - | - | - | - | 159.83 | 65.67 | - | - | - |
| K3 | 0.72 | 5.08 | 14.59 | 0.34 | 2.39 | - | - | - | - | 189.47 | 84.94 | - | - | - |
| K2 | 0.68 | 4.51 | 15.98 | 0.32 | 2.54 | - | - | - | - | 199.95 | 84.65 | - | - | - |
| U77 | 0.65 | 4.01 | 10.08 | 0.62 | 6.98 | - | - | - | - | 150.69 | 54.90 | - | - | - |
| U44 | 0.63 | 3.64 | 11.19 | 0.45 | 4.26 | - | - | - | - | 123.64 | 47.16 | - | - | - |
| ML34 | 0.58 | 2.12 | - | - | - | - | - | - | - | 12.38 | 2.10 | 1.07 | 0.57 | 0.85 |
| Marker 9 | 0.56 | 1.67 | 8.89 | 0.53 | - | 1.80 | - | - | - | - | - | - | - | - |
| U47 | 0.80 | 4.70 | 18.24 | - | - | - | - | - | - | 120.05 | 52.37 | - | - | - |
| U73 | 0.82 | 4.61 | 19.55 | - | - | - | - | - | - | 137.15 | 46.89 | - | - | - |
| U78 | 0.79 | 4.10 | 16.52 | - | - | - | - | - | - | 146.81 | 47.16 | - | - | - |
| K1 | 0.79 | 3.93 | 15.47 | - | - | - | - | - | - | 90.84 | 34.87 | - | - | - |
| K25 | 0.63 | 3.02 | 9.95 | - | - | - | - | - | - | 72.80 | 23.20 | - | - | - |
| ML20 | 0.44 | 1.21 | - | - | - | - | - | - | - | 10.31 | 1.13 | 1.31 | - | - |
| ML63 | - | - | - | - | - | - | - | - | - | 10.97 | 2.25 | 1.24 | 0.38 | 0.92 |
| ML47 | - | - | - | - | - | - | - | - | - | 10.96 | 2.20 | 1.25 | 0.84 | 1.01 |
| BC-G | 0.33 | 0.76 | - | 0.61 | - | 2.52 | - | - | - | - | - | - | - | - |
| Stagreef | 0.44 | 1.13 | - | 0.63 | - | 2.49 | - | - | - | - | - | - | - | - |
| Sunny Isles-F | 0.40 | 1.00 | - | 0.56 | - | 2.02 | - | - | - | - | - | - | - | - |
| BC-H | 0.56 | 1.61 | - | 0.50 | - | 1.58 | - | - | - | - | - | - | - | - |
| ML5 | 0.59 | 2.82 | 5.50 | - | - | - | - | - | - | 63.40 | - | - | - | - |
| ML56 | 0.48 | 2.18 | 3.38 | - | - | - | - | - | - | 22.90 | - | - | - | - |
| ML54 | 0.48 | 1.87 | 3.99 | - | - | - | - | - | - | 34.10 | - | - | - | - |
| U25 | 0.26 | - | 1.63 | 0.61 | 5.38 | - | - | - | - | - | - | - | - | - |
| FM20 | - | - | - | 0.59 | 16.16 | 8.02 | - | - | - | - | - | - | - | - |
| B | 0.78 | 3.61 | 18.89 | - | - | - | - | - | - | - | - | - | - | - |
| DR-A | 0.49 | 2.45 | 5.40 | - | - | - | - | - | - | - | - | - | - | - |
| THIN | 0.55 | 2.19 | 6.78 | - | - | - | - | - | - | - | - | - | - | - |
| Acerv 1 (A-AC) | 0.59 | 2.00 | 7.89 | - | - | - | - | - | - | - | - | - | - | - |
| ELK | 0.50 | 1.74 | 5.36 | - | - | - | - | - | - | - | - | - | - | - |
| G1 | 0.49 | 1.66 | 5.27 | - | - | - | - | - | - | - | - | - | - | - |
| Struggle Bus | 0.52 | 1.66 | 9.27 | - | - | - | - | - | - | - | - | - | - | - |
| Acerv 3 (C-AC) | 0.55 | 1.63 | 7.82 | - | - | - | - | - | - | - | - | - | - | - |
| Acerv 2 (B-AC) | 0.54 | 1.61 | 5.26 | - | - | - | - | - | - | - | - | - | - | - |
| Site 406 | 0.52 | 1.61 | 8.05 | - | - | - | - | - | - | - | - | - | - | - |
| G16 | 0.55 | 1.58 | 6.75 | - | - | - | - | - | - | - | - | - | - | - |
| TT (Thicket 3) | 0.48 | 1.53 | 3.25 | - | - | - | - | - | - | - | - | - | - | - |
| FM12 | 0.38 | 1.50 | 1.33 | - | - | - | - | - | - | - | - | - | - | - |
| Acerv 5 (E-AC) | 0.46 | 1.46 | 7.24 | - | - | - | - | - | - | - | - | - | - | - |
| G17 | 0.54 | 1.43 | 6.39 | - | - | - | - | - | - | - | - | - | - | - |
| ML4 | 0.42 | 1.38 | 3.82 | - | - | - | - | - | - | - | - | - | - | - |
| U24 | 0.42 | 1.33 | 3.84 | - | - | - | - | - | - | - | - | - | - | - |
| Steph’s | 0.52 | 1.33 | 10.34 | - | - | - | - | - | - | - | - | - | - | - |
| Trans 2 | 0.52 | 1.27 | 7.51 | - | - | - | - | - | - | - | - | - | - | - |
| THICK | 0.38 | 1.27 | 2.87 | - | - | - | - | - | - | - | - | - | - | - |
| Grounding | 0.45 | 1.26 | 5.07 | - | - | - | - | - | - | - | - | - | - | - |
| G11 | 0.42 | 1.26 | 3.78 | - | - | - | - | - | - | - | - | - | - | - |
| Dom’s Reef | 0.57 | 1.25 | 9.31 | - | - | - | - | - | - | - | - | - | - | - |
| G6 | 0.39 | 1.15 | 3.82 | - | - | - | - | - | - | - | - | - | - | - |
| Cooper’s | 0.45 | 1.12 | 4.53 | - | - | - | - | - | - | - | - | - | - | - |
| Inshore | 0.40 | 1.09 | 4.08 | - | - | - | - | - | - | - | - | - | - | - |
| FM5 | 0.26 | 1.08 | 3.10 | - | - | - | - | - | - | - | - | - | - | - |
| Trav’s Reef | 0.54 | 1.05 | 7.62 | - | - | - | - | - | - | - | - | - | - | - |
| FM7 | 0.25 | 1.05 | 1.97 | - | - | - | - | - | - | - | - | - | - | - |
| Britt’s Reef | 0.47 | 1.01 | 9.59 | - | - | - | - | - | - | - | - | - | - | - |
| FM18 | 0.30 | 0.91 | 2.08 | - | - | - | - | - | - | - | - | - | - | - |
| FM13 | 0.25 | 0.90 | 1.78 | - | - | - | - | - | - | - | - | - | - | - |
| FM1 | 0.24 | 0.90 | 4.37 | - | - | - | - | - | - | - | - | - | - | - |
| FM10 | 0.39 | 0.89 | 2.48 | - | - | - | - | - | - | - | - | - | - | - |
| Almost Done | 0.41 | 0.87 | 6.22 | - | - | - | - | - | - | - | - | - | - | - |
| Ford’s Reef | 0.52 | 0.86 | 10.78 | - | - | - | - | - | - | - | - | - | - | - |
| G15 | 0.47 | 0.86 | 5.03 | - | - | - | - | - | - | - | - | - | - | - |
| G2 | 0.42 | 0.85 | 4.38 | - | - | - | - | - | - | - | - | - | - | - |
| Acerv 4 (D-AC) | 0.54 | 0.84 | 7.05 | - | - | - | - | - | - | - | - | - | - | - |
| MUTANT182 | 0.42 | 0.83 | 3.83 | - | - | - | - | - | - | - | - | - | - | - |
| Alina-B | 0.53 | 0.82 | 6.81 | - | - | - | - | - | - | - | - | - | - | - |
| Alina-A | 0.59 | 0.70 | 7.81 | - | - | - | - | - | - | - | - | - | - | - |
| Big Bertha | 0.45 | 0.70 | 5.20 | - | - | - | - | - | - | - | - | - | - | - |
| Fowey | 0.47 | 0.60 | 6.29 | - | - | - | - | - | - | - | - | - | - | - |
| Navassa | 0.33 | 0.59 | 2.34 | - | - | - | - | - | - | - | - | - | - | - |
| B/B | 0.38 | 0.58 | 2.94 | - | - | - | - | - | - | - | - | - | - | - |
| Trans 1 | 0.38 | 0.56 | 4.82 | - | - | - | - | - | - | - | - | - | - | - |
| FM9 | 0.35 | 0.54 | 2.27 | - | - | - | - | - | - | - | - | - | - | - |
| G18 | 0.24 | 0.51 | 1.64 | - | - | - | - | - | - | - | - | - | - | - |
| North Midchannel-A | 0.68 | 0.49 | 9.07 | - | - | - | - | - | - | - | - | - | - | - |
| W/Y | 0.21 | 0.40 | 2.47 | - | - | - | - | - | - | - | - | - | - | - |
| W/G | 0.31 | 0.34 | 7.10 | - | - | - | - | - | - | - | - | - | - | - |
| W/B | 0.29 | 0.30 | 3.51 | - | - | - | - | - | - | - | - | - | - | - |
| Sunny Isles-A | 0.90 | 4.50 | - | - | - | - | - | - | - | - | - | - | - | - |
| Stag-B | 0.86 | 4.05 | - | - | - | - | - | - | - | - | - | - | - | - |
| MB-C | 0.86 | 3.90 | - | - | - | - | - | - | - | - | - | - | - | - |
| MB-A | 0.85 | 3.83 | - | - | - | - | - | - | - | - | - | - | - | - |
| BC-8A | 0.83 | 3.79 | - | - | - | - | - | - | - | - | - | - | - | - |
| Cheetos-C | 0.83 | 3.71 | - | - | - | - | - | - | - | - | - | - | - | - |
| MB-B | 0.78 | 3.39 | - | - | - | - | - | - | - | - | - | - | - | - |
| Sunny Isles-C | 0.78 | 3.38 | - | - | - | - | - | - | - | - | - | - | - | - |
| Stag-A | 0.78 | 3.31 | - | - | - | - | - | - | - | - | - | - | - | - |
| BC-8B | 0.79 | 3.30 | - | - | - | - | - | - | - | - | - | - | - | - |
| Cheetos-D | 0.74 | 3.15 | - | - | - | - | - | - | - | - | - | - | - | - |
| BC-11 | 0.73 | 3.01 | - | - | - | - | - | - | - | - | - | - | - | - |
| Tuna Jelly-B | 0.79 | 2.95 | - | - | - | - | - | - | - | - | - | - | - | - |
| MB-D | 0.73 | 2.88 | - | - | - | - | - | - | - | - | - | - | - | - |
| Sunny Isles-B | 0.71 | 2.82 | - | - | - | - | - | - | - | - | - | - | - | - |
| Sunny Isles-D | 0.68 | 2.73 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM17 | 0.65 | 2.50 | - | - | - | - | - | - | - | - | - | - | - | - |
| Tuna Jelly-A | 0.71 | 2.46 | - | - | - | - | - | - | - | - | - | - | - | - |
| Yung’s-B | 0.66 | 2.45 | - | - | - | - | - | - | - | - | - | - | - | - |
| Kelsey-1 | 0.63 | 2.38 | - | - | - | - | - | - | - | - | - | - | - | - |
| Yung’s-A | 0.62 | 2.36 | - | - | - | - | - | - | - | - | - | - | - | - |
| Kelsey-2 | 0.63 | 2.33 | - | - | - | - | - | - | - | - | - | - | - | - |
| BC-1 | 0.61 | 2.26 | - | - | - | - | - | - | - | - | - | - | - | - |
| Cheetos-A | 0.61 | 2.25 | - | - | - | - | - | - | - | - | - | - | - | - |
| ML48 | 0.63 | 2.24 | - | - | - | - | - | - | - | - | - | - | - | - |
| Site 211 | 0.56 | 1.64 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM15 | 0.26 | 1.62 | - | - | - | - | - | - | - | - | - | - | - | - |
| MB | 0.52 | 1.61 | - | - | - | - | - | - | - | - | - | - | - | - |
| Govt Cut | 0.55 | 1.58 | - | - | - | - | - | - | - | - | - | - | - | - |
| Cheetos-B | 0.42 | 1.37 | - | - | - | - | - | - | - | - | - | - | - | - |
| ML14 | 0.50 | 1.35 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM16 | 0.32 | 1.34 | - | - | - | - | - | - | - | - | - | - | - | - |
| Jons | 0.45 | 1.26 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM3 | 0.22 | 0.80 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM11 | 0.22 | 0.80 | - | - | - | - | - | - | - | - | - | - | - | - |
| FM19 | 0.24 | 0.47 | - | - | - | - | - | - | - | - | - | - | - | - |
| ML38 | - | - | 3.66 | - | - | - | - | - | - | 43.80 | - | - | - | - |
| ML43 | - | - | 2.59 | - | - | - | - | - | - | 29.97 | - | - | - | - |
| ML11 | 0.25 | - | 1.01 | - | - | - | - | - | - | - | - | - | - | - |
| M10 | - | - | - | - | - | - | - | - | - | 34.88 | 2.23 | - | - | - |
| B8 | - | - | - | - | - | - | - | - | - | 22.40 | 1.32 | - | - | - |
| M1 | - | - | - | - | - | - | - | - | - | 10.38 | 0.58 | - | - | - |
Because each of these metrics describe a different component of coral growth and are measured on different scales, they cannot be directly aggregated. Instead, we must first calculate standardized scores for each metric prior to aligning disparate measurements. I chose to standardize by calculating z-scores where the difference of each value and the column mean is divided by the column’s standard deviation. Thus, the column mean is now 0 and the standard deviation is 1. Each resulting value indicates the amount of standard deviations about the mean for that metric.
I then group together all linear extension metrics to calculate a genotype’s average standard deviation about the mean and impute this value for all missing linear extension metrics. I do the same for calcification metrics. If no calcification or no linear extension metrics exist for a particular genotype, then 0’s are imputed for all calcification or no linear extension metrics, which signifies average performance.
The table below shows the resulting standardized data with scores in black indicating calculated z-scores, scores in blue indicating imputed z-scores based on the other linear extension or calcification scores, and scores in red indicating imputed scores of 0 if no linear extension or calcification data was available.| genotype | specific growth rate | 6-month linear growth | annual linear growth | colony volumetric SGR | annual colony volumetric growth | 6-month colony volumetric growth | 6-month interstitial space growth | annual interstitial space growth | interstitial space SGR | daily calcification | mass normalized daily calcification | SA normalized daily calcification | dark calcification | light calcification |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ML41 | -0.73 | -0.49 | -0.57 | -0.39 | -0.54 | -0.01 | 0.06 | -0.89 | 0.45 | -0.6 | -0.68 | -0.33 | 1.26 | -0.22 |
| ML7 | -0.95 | -0.77 | -0.68 | 0.43 | 0.39 | -0.26 | 0.53 | 1.51 | 1.41 | -0.39 | -0.66 | 0.61 | 0.25 | 0.3 |
| ML62 | 0.24 | 0.17 | -0.35 | -0.01 | 0.22 | -0.35 | 0.99 | 1.33 | 0.92 | -0.8 | -0.68 | -1.42 | -1.27 | -0.06 |
| ML50 | -0.06 | -0.02 | -0.17 | -0.7 | 0.04 | -0.45 | 0.33 | 1.25 | -0.59 | -0.78 | -0.67 | 0.65 | 0.86 | -1.11 |
| ML31 | -0.52 | -0.02 | -0.46 | -1.53 | -0.94 | -0.46 | 0.11 | -0.94 | -1.1 | -0.63 | -0.68 | -0.31 | 1.31 | 0.19 |
| ML3 | -0.53 | -0.16 | -0.43 | -0.6 | -0.23 | -0.47 | -0.39 | -0.52 | -1.07 | -0.8 | -0.68 | -0.63 | 0.28 | -1.33 |
| ML44 | -0.53 | -0.63 | -0.43 | 0.07 | 0.12 | -0.59 | -1.51 | -0.78 | -1.22 | -0.61 | -0.68 | 0.27 | -0.28 | 1.41 |
| ML1 | -0.45 | -0.33 | -0.6 | -0.66 | -0.38 | -0.59 | -1.81 | -0.74 | -0.23 | -0.7 | -0.7 | 1.51 | -0.35 | -1.69 |
| ML13 | -0.34 | -0.51 | -0.69 | -1.48 | -0.88 | -0.69 | 0.37 | -0.46 | 0.13 | -0.84 | -0.7 | -1.93 | -0.28 | 0.25 |
| ML36 | -0.76 | -0.79 | -0.64 | -0.01 | -0.03 | -0.36 | 1.33 | 0.24 | 1.3 | 0 | 0 | 0 | 0 | 0 |
| M6 | 0.27 | -0.15 | 0.82 | 0.48 | 1.78 | 1.7 | 0.82 | 0.82 | 0.82 | -0.75 | -0.72 | -0.73 | -0.73 | -0.73 |
| U41 | 1.05 | 3.07 | 1.64 | 0.56 | -0.18 | 1.23 | 1.23 | 1.23 | 1.23 | 1.68 | 1.57 | 1.63 | 1.63 | 1.63 |
| K3 | 1.18 | 2.7 | 1.95 | -1.66 | -1.04 | 0.63 | 0.63 | 0.63 | 0.63 | 2.17 | 2.25 | 2.21 | 2.21 | 2.21 |
| K2 | 0.94 | 2.21 | 2.28 | -1.78 | -0.99 | 0.53 | 0.53 | 0.53 | 0.53 | 2.34 | 2.24 | 2.29 | 2.29 | 2.29 |
| U77 | 0.74 | 1.79 | 0.88 | 1.34 | 0.31 | 1.01 | 1.01 | 1.01 | 1.01 | 1.53 | 1.19 | 1.36 | 1.36 | 1.36 |
| U44 | 0.61 | 1.48 | 1.15 | -0.47 | -0.49 | 0.45 | 0.45 | 0.45 | 0.45 | 1.08 | 0.92 | 1 | 1 | 1 |
| ML34 | 0.35 | 0.2 | 0.28 | 0.28 | 0.28 | 0.28 | 0.28 | 0.28 | 0.28 | -0.76 | -0.68 | -0.73 | -0.75 | 0.03 |
| Marker 9 | 0.2 | -0.19 | 0.6 | 0.45 | 0.15 | -0.31 | 0.15 | 0.15 | 0.15 | 0 | 0 | 0 | 0 | 0 |
| U47 | 1.66 | 2.37 | 2.82 | 2.28 | 2.28 | 2.28 | 2.28 | 2.28 | 2.28 | 1.02 | 1.1 | 1.06 | 1.06 | 1.06 |
| U73 | 1.74 | 2.3 | 3.13 | 2.39 | 2.39 | 2.39 | 2.39 | 2.39 | 2.39 | 1.3 | 0.91 | 1.11 | 1.11 | 1.11 |
| U78 | 1.55 | 1.87 | 2.41 | 1.94 | 1.94 | 1.94 | 1.94 | 1.94 | 1.94 | 1.46 | 0.92 | 1.19 | 1.19 | 1.19 |
| K1 | 1.56 | 1.72 | 2.16 | 1.81 | 1.81 | 1.81 | 1.81 | 1.81 | 1.81 | 0.54 | 0.48 | 0.51 | 0.51 | 0.51 |
| K25 | 0.63 | 0.96 | 0.85 | 0.81 | 0.81 | 0.81 | 0.81 | 0.81 | 0.81 | 0.24 | 0.07 | 0.16 | 0.16 | 0.16 |
| ML20 | -0.51 | -0.58 | -0.54 | -0.54 | -0.54 | -0.54 | -0.54 | -0.54 | -0.54 | -0.79 | -0.71 | 1.12 | -0.13 | -0.13 |
| ML63 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | -0.78 | -0.67 | 0.56 | -1.9 | 0.66 |
| ML47 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | -0.78 | -0.67 | 0.63 | 0.86 | 1.57 |
| BC-G | -1.11 | -0.96 | -0.17 | 1.29 | -0.17 | 0.11 | -0.17 | -0.17 | -0.17 | 0 | 0 | 0 | 0 | 0 |
| Stagreef | -0.5 | -0.65 | 0.11 | 1.5 | 0.11 | 0.09 | 0.11 | 0.11 | 0.11 | 0 | 0 | 0 | 0 | 0 |
| Sunny Isles-F | -0.75 | -0.76 | -0.24 | 0.73 | -0.24 | -0.18 | -0.24 | -0.24 | -0.24 | 0 | 0 | 0 | 0 | 0 |
| BC-H | 0.2 | -0.24 | -0.09 | 0.12 | -0.09 | -0.43 | -0.09 | -0.09 | -0.09 | 0 | 0 | 0 | 0 | 0 |
| ML5 | 0.38 | 0.78 | -0.2 | 0.32 | 0.32 | 0.32 | 0.32 | 0.32 | 0.32 | 0.09 | 0.09 | 0.09 | 0.09 | 0.09 |
| ML56 | -0.24 | 0.24 | -0.7 | -0.23 | -0.23 | -0.23 | -0.23 | -0.23 | -0.23 | -0.58 | -0.58 | -0.58 | -0.58 | -0.58 |
| ML54 | -0.25 | -0.02 | -0.56 | -0.27 | -0.27 | -0.27 | -0.27 | -0.27 | -0.27 | -0.4 | -0.4 | -0.4 | -0.4 | -0.4 |
| U25 | -1.53 | -0.39 | -1.12 | 1.23 | -0.16 | -0.39 | -0.39 | -0.39 | -0.39 | 0 | 0 | 0 | 0 | 0 |
| FM20 | 2.45 | 2.45 | 2.45 | 1.09 | 3 | 3.26 | 2.45 | 2.45 | 2.45 | 0 | 0 | 0 | 0 | 0 |
| B | 1.51 | 1.46 | 2.97 | 1.98 | 1.98 | 1.98 | 1.98 | 1.98 | 1.98 | 0 | 0 | 0 | 0 | 0 |
| DR-A | -0.17 | 0.47 | -0.22 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0 | 0 | 0 | 0 | 0 |
| THIN | 0.19 | 0.25 | 0.1 | 0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0 | 0 | 0 | 0 | 0 |
| Acerv 1 (A-AC) | 0.41 | 0.09 | 0.36 | 0.29 | 0.29 | 0.29 | 0.29 | 0.29 | 0.29 | 0 | 0 | 0 | 0 | 0 |
| ELK | -0.12 | -0.13 | -0.23 | -0.16 | -0.16 | -0.16 | -0.16 | -0.16 | -0.16 | 0 | 0 | 0 | 0 | 0 |
| G1 | -0.16 | -0.2 | -0.26 | -0.21 | -0.21 | -0.21 | -0.21 | -0.21 | -0.21 | 0 | 0 | 0 | 0 | 0 |
| Struggle Bus | -0.01 | -0.2 | 0.69 | 0.16 | 0.16 | 0.16 | 0.16 | 0.16 | 0.16 | 0 | 0 | 0 | 0 | 0 |
| Acerv 3 (C-AC) | 0.18 | -0.22 | 0.35 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0 | 0 | 0 | 0 | 0 |
| Acerv 2 (B-AC) | 0.08 | -0.24 | -0.26 | -0.14 | -0.14 | -0.14 | -0.14 | -0.14 | -0.14 | 0 | 0 | 0 | 0 | 0 |
| Site 406 | -0.03 | -0.24 | 0.4 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0 | 0 | 0 | 0 | 0 |
| G16 | 0.17 | -0.26 | 0.09 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| TT (Thicket 3) | -0.25 | -0.3 | -0.73 | -0.43 | -0.43 | -0.43 | -0.43 | -0.43 | -0.43 | 0 | 0 | 0 | 0 | 0 |
| FM12 | -0.83 | -0.33 | -1.19 | -0.78 | -0.78 | -0.78 | -0.78 | -0.78 | -0.78 | 0 | 0 | 0 | 0 | 0 |
| Acerv 5 (E-AC) | -0.38 | -0.37 | 0.21 | -0.18 | -0.18 | -0.18 | -0.18 | -0.18 | -0.18 | 0 | 0 | 0 | 0 | 0 |
| G17 | 0.1 | -0.39 | 0.01 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | 0 | 0 | 0 | 0 | 0 |
| ML4 | -0.62 | -0.44 | -0.6 | -0.55 | -0.55 | -0.55 | -0.55 | -0.55 | -0.55 | 0 | 0 | 0 | 0 | 0 |
| U24 | -0.62 | -0.47 | -0.59 | -0.56 | -0.56 | -0.56 | -0.56 | -0.56 | -0.56 | 0 | 0 | 0 | 0 | 0 |
| Steph’s | 0 | -0.47 | 0.94 | 0.16 | 0.16 | 0.16 | 0.16 | 0.16 | 0.16 | 0 | 0 | 0 | 0 | 0 |
| Trans 2 | 0.01 | -0.53 | 0.28 | -0.08 | -0.08 | -0.08 | -0.08 | -0.08 | -0.08 | 0 | 0 | 0 | 0 | 0 |
| THICK | -0.83 | -0.53 | -0.82 | -0.73 | -0.73 | -0.73 | -0.73 | -0.73 | -0.73 | 0 | 0 | 0 | 0 | 0 |
| Grounding | -0.43 | -0.53 | -0.3 | -0.42 | -0.42 | -0.42 | -0.42 | -0.42 | -0.42 | 0 | 0 | 0 | 0 | 0 |
| G11 | -0.63 | -0.54 | -0.61 | -0.59 | -0.59 | -0.59 | -0.59 | -0.59 | -0.59 | 0 | 0 | 0 | 0 | 0 |
| Dom’s Reef | 0.3 | -0.54 | 0.7 | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 | 0 | 0 | 0 | 0 | 0 |
| G6 | -0.76 | -0.63 | -0.6 | -0.66 | -0.66 | -0.66 | -0.66 | -0.66 | -0.66 | 0 | 0 | 0 | 0 | 0 |
| Cooper’s | -0.42 | -0.66 | -0.43 | -0.5 | -0.5 | -0.5 | -0.5 | -0.5 | -0.5 | 0 | 0 | 0 | 0 | 0 |
| Inshore | -0.7 | -0.68 | -0.54 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | 0 | 0 | 0 | 0 | 0 |
| FM5 | -1.57 | -0.69 | -0.77 | -1.01 | -1.01 | -1.01 | -1.01 | -1.01 | -1.01 | 0 | 0 | 0 | 0 | 0 |
| Trav’s Reef | 0.1 | -0.71 | 0.3 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | 0 | 0 | 0 | 0 | 0 |
| FM7 | -1.6 | -0.71 | -1.04 | -1.12 | -1.12 | -1.12 | -1.12 | -1.12 | -1.12 | 0 | 0 | 0 | 0 | 0 |
| Britt’s Reef | -0.32 | -0.75 | 0.77 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | 0 | 0 | 0 | 0 | 0 |
| FM18 | -1.33 | -0.83 | -1.01 | -1.06 | -1.06 | -1.06 | -1.06 | -1.06 | -1.06 | 0 | 0 | 0 | 0 | 0 |
| FM13 | -1.63 | -0.84 | -1.08 | -1.18 | -1.18 | -1.18 | -1.18 | -1.18 | -1.18 | 0 | 0 | 0 | 0 | 0 |
| FM1 | -1.65 | -0.84 | -0.47 | -0.99 | -0.99 | -0.99 | -0.99 | -0.99 | -0.99 | 0 | 0 | 0 | 0 | 0 |
| FM10 | -0.76 | -0.85 | -0.91 | -0.84 | -0.84 | -0.84 | -0.84 | -0.84 | -0.84 | 0 | 0 | 0 | 0 | 0 |
| Almost Done | -0.68 | -0.86 | -0.03 | -0.52 | -0.52 | -0.52 | -0.52 | -0.52 | -0.52 | 0 | 0 | 0 | 0 | 0 |
| Ford’s Reef | -0.03 | -0.87 | 1.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0 | 0 | 0 | 0 | 0 |
| G15 | -0.3 | -0.87 | -0.31 | -0.49 | -0.49 | -0.49 | -0.49 | -0.49 | -0.49 | 0 | 0 | 0 | 0 | 0 |
| G2 | -0.58 | -0.88 | -0.47 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | 0 | 0 | 0 | 0 | 0 |
| Acerv 4 (D-AC) | 0.11 | -0.89 | 0.17 | -0.2 | -0.2 | -0.2 | -0.2 | -0.2 | -0.2 | 0 | 0 | 0 | 0 | 0 |
| MUTANT182 | -0.6 | -0.9 | -0.6 | -0.7 | -0.7 | -0.7 | -0.7 | -0.7 | -0.7 | 0 | 0 | 0 | 0 | 0 |
| Alina-B | 0.03 | -0.91 | 0.11 | -0.26 | -0.26 | -0.26 | -0.26 | -0.26 | -0.26 | 0 | 0 | 0 | 0 | 0 |
| Alina-A | 0.38 | -1.01 | 0.35 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | -0.1 | 0 | 0 | 0 | 0 | 0 |
| Big Bertha | -0.43 | -1.01 | -0.27 | -0.57 | -0.57 | -0.57 | -0.57 | -0.57 | -0.57 | 0 | 0 | 0 | 0 | 0 |
| Fowey | -0.31 | -1.1 | -0.01 | -0.47 | -0.47 | -0.47 | -0.47 | -0.47 | -0.47 | 0 | 0 | 0 | 0 | 0 |
| Navassa | -1.16 | -1.1 | -0.95 | -1.07 | -1.07 | -1.07 | -1.07 | -1.07 | -1.07 | 0 | 0 | 0 | 0 | 0 |
| B/B | -0.85 | -1.11 | -0.81 | -0.92 | -0.92 | -0.92 | -0.92 | -0.92 | -0.92 | 0 | 0 | 0 | 0 | 0 |
| Trans 1 | -0.85 | -1.13 | -0.36 | -0.78 | -0.78 | -0.78 | -0.78 | -0.78 | -0.78 | 0 | 0 | 0 | 0 | 0 |
| FM9 | -1.04 | -1.14 | -0.97 | -1.05 | -1.05 | -1.05 | -1.05 | -1.05 | -1.05 | 0 | 0 | 0 | 0 | 0 |
| G18 | -1.65 | -1.17 | -1.12 | -1.31 | -1.31 | -1.31 | -1.31 | -1.31 | -1.31 | 0 | 0 | 0 | 0 | 0 |
| North Midchannel-A | 0.92 | -1.19 | 0.64 | 0.13 | 0.13 | 0.13 | 0.13 | 0.13 | 0.13 | 0 | 0 | 0 | 0 | 0 |
| W/Y | -1.85 | -1.27 | -0.92 | -1.34 | -1.34 | -1.34 | -1.34 | -1.34 | -1.34 | 0 | 0 | 0 | 0 | 0 |
| W/G | -1.26 | -1.31 | 0.18 | -0.8 | -0.8 | -0.8 | -0.8 | -0.8 | -0.8 | 0 | 0 | 0 | 0 | 0 |
| W/B | -1.4 | -1.35 | -0.67 | -1.14 | -1.14 | -1.14 | -1.14 | -1.14 | -1.14 | 0 | 0 | 0 | 0 | 0 |
| Sunny Isles-A | 2.2 | 2.2 | 2.2 | 2.2 | 2.2 | 2.2 | 2.2 | 2.2 | 2.2 | 0 | 0 | 0 | 0 | 0 |
| Stag-B | 1.97 | 1.83 | 1.9 | 1.9 | 1.9 | 1.9 | 1.9 | 1.9 | 1.9 | 0 | 0 | 0 | 0 | 0 |
| MB-C | 1.97 | 1.7 | 1.84 | 1.84 | 1.84 | 1.84 | 1.84 | 1.84 | 1.84 | 0 | 0 | 0 | 0 | 0 |
| MB-A | 1.91 | 1.64 | 1.78 | 1.78 | 1.78 | 1.78 | 1.78 | 1.78 | 1.78 | 0 | 0 | 0 | 0 | 0 |
| BC-8A | 1.81 | 1.61 | 1.71 | 1.71 | 1.71 | 1.71 | 1.71 | 1.71 | 1.71 | 0 | 0 | 0 | 0 | 0 |
| Cheetos-C | 1.81 | 1.54 | 1.68 | 1.68 | 1.68 | 1.68 | 1.68 | 1.68 | 1.68 | 0 | 0 | 0 | 0 | 0 |
| MB-B | 1.5 | 1.26 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 0 | 0 | 0 | 0 | 0 |
| Sunny Isles-C | 1.5 | 1.26 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 1.38 | 0 | 0 | 0 | 0 | 0 |
| Stag-A | 1.49 | 1.2 | 1.34 | 1.34 | 1.34 | 1.34 | 1.34 | 1.34 | 1.34 | 0 | 0 | 0 | 0 | 0 |
| BC-8B | 1.55 | 1.19 | 1.37 | 1.37 | 1.37 | 1.37 | 1.37 | 1.37 | 1.37 | 0 | 0 | 0 | 0 | 0 |
| Cheetos-D | 1.26 | 1.07 | 1.16 | 1.16 | 1.16 | 1.16 | 1.16 | 1.16 | 1.16 | 0 | 0 | 0 | 0 | 0 |
| BC-11 | 1.24 | 0.95 | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 | 0 | 0 | 0 | 0 | 0 |
| Tuna Jelly-B | 1.56 | 0.9 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 0 | 0 | 0 | 0 | 0 |
| MB-D | 1.22 | 0.83 | 1.03 | 1.03 | 1.03 | 1.03 | 1.03 | 1.03 | 1.03 | 0 | 0 | 0 | 0 | 0 |
| Sunny Isles-B | 1.13 | 0.79 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0 | 0 | 0 | 0 | 0 |
| Sunny Isles-D | 0.93 | 0.71 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0 | 0 | 0 | 0 | 0 |
| FM17 | 0.73 | 0.52 | 0.62 | 0.62 | 0.62 | 0.62 | 0.62 | 0.62 | 0.62 | 0 | 0 | 0 | 0 | 0 |
| Tuna Jelly-A | 1.08 | 0.48 | 0.78 | 0.78 | 0.78 | 0.78 | 0.78 | 0.78 | 0.78 | 0 | 0 | 0 | 0 | 0 |
| Yung’s-B | 0.8 | 0.47 | 0.63 | 0.63 | 0.63 | 0.63 | 0.63 | 0.63 | 0.63 | 0 | 0 | 0 | 0 | 0 |
| Kelsey-1 | 0.61 | 0.41 | 0.51 | 0.51 | 0.51 | 0.51 | 0.51 | 0.51 | 0.51 | 0 | 0 | 0 | 0 | 0 |
| Yung’s-A | 0.56 | 0.39 | 0.48 | 0.48 | 0.48 | 0.48 | 0.48 | 0.48 | 0.48 | 0 | 0 | 0 | 0 | 0 |
| Kelsey-2 | 0.62 | 0.37 | 0.49 | 0.49 | 0.49 | 0.49 | 0.49 | 0.49 | 0.49 | 0 | 0 | 0 | 0 | 0 |
| BC-1 | 0.52 | 0.31 | 0.41 | 0.41 | 0.41 | 0.41 | 0.41 | 0.41 | 0.41 | 0 | 0 | 0 | 0 | 0 |
| Cheetos-A | 0.49 | 0.3 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 | 0 | 0 | 0 | 0 | 0 |
| ML48 | 0.64 | 0.29 | 0.47 | 0.47 | 0.47 | 0.47 | 0.47 | 0.47 | 0.47 | 0 | 0 | 0 | 0 | 0 |
| Site 211 | 0.24 | -0.21 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0 | 0 | 0 | 0 | 0 |
| FM15 | -1.56 | -0.23 | -0.9 | -0.9 | -0.9 | -0.9 | -0.9 | -0.9 | -0.9 | 0 | 0 | 0 | 0 | 0 |
| MB | -0.04 | -0.24 | -0.14 | -0.14 | -0.14 | -0.14 | -0.14 | -0.14 | -0.14 | 0 | 0 | 0 | 0 | 0 |
| Govt Cut | 0.17 | -0.27 | -0.05 | -0.05 | -0.05 | -0.05 | -0.05 | -0.05 | -0.05 | 0 | 0 | 0 | 0 | 0 |
| Cheetos-B | -0.59 | -0.44 | -0.52 | -0.52 | -0.52 | -0.52 | -0.52 | -0.52 | -0.52 | 0 | 0 | 0 | 0 | 0 |
| ML14 | -0.14 | -0.46 | -0.3 | -0.3 | -0.3 | -0.3 | -0.3 | -0.3 | -0.3 | 0 | 0 | 0 | 0 | 0 |
| FM16 | -1.2 | -0.47 | -0.84 | -0.84 | -0.84 | -0.84 | -0.84 | -0.84 | -0.84 | 0 | 0 | 0 | 0 | 0 |
| Jons | -0.43 | -0.53 | -0.48 | -0.48 | -0.48 | -0.48 | -0.48 | -0.48 | -0.48 | 0 | 0 | 0 | 0 | 0 |
| FM3 | -1.77 | -0.92 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | 0 | 0 | 0 | 0 | 0 |
| FM11 | -1.76 | -0.93 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | -1.35 | 0 | 0 | 0 | 0 | 0 |
| FM19 | -1.64 | -1.2 | -1.42 | -1.42 | -1.42 | -1.42 | -1.42 | -1.42 | -1.42 | 0 | 0 | 0 | 0 | 0 |
| ML38 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.64 | -0.24 | -0.24 | -0.24 | -0.24 | -0.24 |
| ML43 | -0.89 | -0.89 | -0.89 | -0.89 | -0.89 | -0.89 | -0.89 | -0.89 | -0.89 | -0.47 | -0.47 | -0.47 | -0.47 | -0.47 |
| ML11 | -1.6 | -1.43 | -1.26 | -1.43 | -1.43 | -1.43 | -1.43 | -1.43 | -1.43 | 0 | 0 | 0 | 0 | 0 |
| M10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | -0.39 | -0.67 | -0.53 | -0.53 | -0.53 |
| B8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | -0.59 | -0.7 | -0.65 | -0.65 | -0.65 |
| M1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | -0.79 | -0.73 | -0.76 | -0.76 | -0.76 |
Now that we have standardized scores for 14 different metrics, we can compare and align metrics into a single, composite index to understand relative genotype performance.
First, I group the growth metrics into their two large determinants of linear extension and calcification and calculate the mean standardized score for each of these determinants of growth.
Then, I individually weight the linear extension and calcification scores. The derivation of the two distinct weights is explained below. The two weights add to 1.
Finally, the two weighted values are added together for a finalized score. For genotypes that only have linear extension data or calcification data, the resulting score is just the weighed linear extension or calcification score. Since average performance has a score of 0 and the two determinants of growth are independently weighed with the sum of the weights equaling 1, the finalized score should best encapsulate true growth rates and permit ranking of relative genotype performance.
This process assumes there is no genotype-effect on density, which is supported by Kuffner et al. (2017) who demonstrated for this species a genotype-specific calcification rate but a plastic density based on its nursery grow out structure.
Weights were determined by characteristic growth of the species, a common practice in calicification budgets of coral reefs. Briefly, calcification is the product of densification and linear extension, and is the total metric we are trying to describe. We have metrics that measure calcification through buoyant weight or total alkalinity anomaly measurements. We also have various determinations of linear extension as it is a common metric captured in the field, but this rapid growth is biased by the quick growing branch tips which is only about 24.6% of the coral’s volume, with the other 75.4% of the coral growing at a rate 10% of the branch tips (data aggregated by Perry Reef Budget, see citations within).
The formula for calculating the gross calcification of a branching A. cervicornis is: \[ G = (l \times c_a \times P \times \rho) + ((l-c_a \times l)\times 0.1 \times P \times \rho) \] where
As you can see, the first term is for the fast linear extension of the branches, and the second term is for the growth of the remaining portion of the colony, growing at a rate 10% of the branch tips. We can combine the constant terms and simplify the equation to:
\[ G = (0.246 \times Q) + (0.754 \times 0.1 \times Q) \] where Q is the terms \(l \times P \times \rho\) combined. Thus the ratio of linear extension to gross calcification is: \[ \frac{\text{LE}}{ G} = \frac{0.246}{0.0754 + 0.246} = \frac{0.246}{0.3214} = 0.7654 \]
Therefore, by measuring linear extension you are describing only 76.54% of the colony growth, while if you measure the calcification, you are describing 100% of the colony’s growth. Our goal is to have these percentages converted to weights which add to 1 to provide simple understanding and calculating of weighted arithmetic means.
\[ 0.7654x + x = 1 \rightarrow 1.7654x =1 \rightarrow x = 1/1.7654 \approx 0.57 \]
Finally, our weighting for calcification measurements take the weight of 0.57 and linear extension measurements take the weight of 1-0.57 or 0.43.
| genotype | score | rank | tercile |
|---|---|---|---|
| U73 | 1.658 | 1 | 1 |
| U47 | 1.587 | 2 | 1 |
| K2 | 1.536 | 3 | 1 |
| K3 | 1.530 | 4 | 1 |
| U78 | 1.515 | 5 | 1 |
| U41 | 1.455 | 6 | 1 |
| U77 | 1.210 | 7 | 1 |
| K1 | 1.072 | 8 | 1 |
| FM20 | 1.054 | 9 | 1 |
| Sunny Isles-A | 0.946 | 10 | 1 |
| B | 0.851 | 11 | 1 |
| Stag-B | 0.817 | 12 | 1 |
| MB-C | 0.790 | 13 | 1 |
| U44 | 0.765 | 14 | 1 |
| MB-A | 0.764 | 15 | 1 |
| BC-8A | 0.736 | 16 | 1 |
| Cheetos-C | 0.721 | 17 | 1 |
| MB-B | 0.594 | 18 | 1 |
| Sunny Isles-C | 0.593 | 19 | 1 |
| BC-8B | 0.588 | 20 | 1 |
| Stag-A | 0.578 | 21 | 1 |
| Tuna Jelly-B | 0.528 | 22 | 1 |
| Cheetos-D | 0.499 | 23 | 1 |
| BC-11 | 0.471 | 24 | 1 |
| MB-D | 0.442 | 25 | 1 |
| K25 | 0.439 | 26 | 1 |
| Sunny Isles-B | 0.411 | 27 | 1 |
| Sunny Isles-D | 0.351 | 28 | 1 |
| Tuna Jelly-A | 0.336 | 29 | 1 |
| Yung’s-B | 0.273 | 30 | 1 |
| FM17 | 0.267 | 31 | 1 |
| Kelsey-1 | 0.219 | 32 | 1 |
| Kelsey-2 | 0.212 | 33 | 1 |
| Yung’s-A | 0.206 | 34 | 1 |
| ML48 | 0.200 | 35 | 1 |
| ML5 | 0.187 | 36 | 1 |
| ML47 | 0.184 | 37 | 1 |
| BC-1 | 0.178 | 38 | 1 |
| Cheetos-A | 0.170 | 39 | 1 |
| Acerv 1 (A-AC) | 0.124 | 40 | 1 |
| ML7 | 0.090 | 41 | 1 |
| THIN | 0.077 | 42 | 1 |
| Struggle Bus | 0.069 | 43 | 1 |
| Steph’s | 0.067 | 44 | 1 |
| Dom’s Reef | 0.066 | 45 | 2 |
| Marker 9 | 0.065 | 46 | 2 |
| North Midchannel-A | 0.054 | 47 | 2 |
| Stagreef | 0.047 | 48 | 2 |
| Acerv 3 (C-AC) | 0.044 | 49 | 2 |
| Ford’s Reef | 0.020 | 50 | 2 |
| Site 406 | 0.018 | 51 | 2 |
| ML36 | 0.013 | 52 | 2 |
| DR-A | 0.012 | 53 | 2 |
| Site 211 | 0.007 | 54 | 2 |
| G16 | 0.000 | 55 | 2 |
| Govt Cut | -0.021 | 56 | 2 |
| Trans 2 | -0.034 | 57 | 2 |
| BC-H | -0.038 | 58 | 2 |
| G17 | -0.041 | 59 | 2 |
| Alina-A | -0.041 | 60 | 2 |
| Britt’s Reef | -0.043 | 61 | 2 |
| Trav’s Reef | -0.045 | 62 | 2 |
| Acerv 2 (B-AC) | -0.059 | 63 | 2 |
| MB | -0.060 | 64 | 2 |
| M6 | -0.067 | 65 | 2 |
| ELK | -0.069 | 66 | 2 |
| BC-G | -0.072 | 67 | 2 |
| Acerv 5 (E-AC) | -0.076 | 68 | 2 |
| Acerv 4 (D-AC) | -0.087 | 69 | 2 |
| G1 | -0.088 | 70 | 2 |
| Sunny Isles-F | -0.103 | 71 | 2 |
| Alina-B | -0.111 | 72 | 2 |
| ML14 | -0.130 | 73 | 2 |
| ML50 | -0.136 | 74 | 2 |
| U25 | -0.169 | 75 | 2 |
| Grounding | -0.180 | 76 | 2 |
| TT (Thicket 3) | -0.184 | 77 | 2 |
| Fowey | -0.203 | 78 | 2 |
| Jons | -0.208 | 79 | 2 |
| ML34 | -0.210 | 80 | 2 |
| G15 | -0.212 | 81 | 2 |
| ML41 | -0.214 | 82 | 2 |
| Cooper’s | -0.216 | 83 | 2 |
| Cheetos-B | -0.223 | 84 | 2 |
| Almost Done | -0.225 | 85 | 2 |
| ML4 | -0.238 | 86 | 2 |
| U24 | -0.241 | 87 | 2 |
| ML63 | -0.243 | 88 | 3 |
| Big Bertha | -0.245 | 89 | 3 |
| ML44 | -0.249 | 90 | 3 |
| G11 | -0.254 | 91 | 3 |
| Inshore | -0.275 | 92 | 3 |
| G2 | -0.277 | 93 | 3 |
| G6 | -0.285 | 94 | 3 |
| ML31 | -0.293 | 95 | 3 |
| MUTANT182 | -0.300 | 96 | 3 |
| M10 | -0.301 | 97 | 3 |
| ML20 | -0.307 | 98 | 3 |
| THICK | -0.313 | 99 | 3 |
| ML62 | -0.332 | 100 | 3 |
| Trans 1 | -0.335 | 101 | 3 |
| FM12 | -0.337 | 102 | 3 |
| W/G | -0.343 | 103 | 3 |
| ML54 | -0.345 | 104 | 3 |
| FM16 | -0.359 | 105 | 3 |
| FM10 | -0.362 | 106 | 3 |
| B8 | -0.369 | 107 | 3 |
| FM15 | -0.385 | 108 | 3 |
| B/B | -0.397 | 109 | 3 |
| ML38 | -0.409 | 110 | 3 |
| FM1 | -0.424 | 111 | 3 |
| ML56 | -0.432 | 112 | 3 |
| M1 | -0.433 | 113 | 3 |
| FM5 | -0.433 | 114 | 3 |
| FM9 | -0.451 | 115 | 3 |
| FM18 | -0.455 | 116 | 3 |
| Navassa | -0.460 | 117 | 3 |
| FM7 | -0.481 | 118 | 3 |
| W/B | -0.490 | 119 | 3 |
| ML1 | -0.496 | 120 | 3 |
| FM13 | -0.508 | 121 | 3 |
| G18 | -0.565 | 122 | 3 |
| ML3 | -0.571 | 123 | 3 |
| W/Y | -0.578 | 124 | 3 |
| FM11 | -0.578 | 125 | 3 |
| FM3 | -0.580 | 126 | 3 |
| FM19 | -0.611 | 127 | 3 |
| ML13 | -0.616 | 128 | 3 |
| ML11 | -0.616 | 129 | 3 |
| ML43 | -0.648 | 130 | 3 |
There is a cluster of the type of metric and the number of metrics (purple), which makes sense as if there are two types of metrics represented, then there is a high likelihood that both calcification and linear extension metrics are represented. However, there is no clustering of the number of metrics and the score. Finally, there is slight clustering of the type of metric and the score (black), with genotypes that have both metrics represented being on average higher than genotypes represented by linear extension or calcification metrics alone.
| contrast | estimate | conf.low | conf.high | adj.p.value |
|---|---|---|---|---|
| G-Both | -4.985 | -7.476 | -2.494 | 0.000 |
| LE-Both | -5.430 | -6.542 | -4.318 | 0.000 |
| LE-G | -0.445 | -2.790 | 1.901 | 0.895 |
| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| (Intercept) | 0.066 | 0.074 | 0.886 | 0.377 |
| metrics | -0.005 | 0.015 | -0.347 | 0.729 |
| contrast | estimate | conf.low | conf.high | adj.p.value |
|---|---|---|---|---|
| G-Both | -0.518 | -1.105 | 0.069 | 0.095 |
| LE-Both | -0.292 | -0.554 | -0.030 | 0.025 |
| LE-G | 0.226 | -0.327 | 0.778 | 0.598 |
We can then dive into the 9 clustered (black) genotypes which are driving this statistically significant difference (have a score >0.5 and have both metrics represented). They all happen to be CRF genotypes used by Katie Lohr in her PhD work at UF and Dan Paradis in his masters work at Auburn. This data is distinguished as only having a few data points in an Auburn lab for buoyant weight measurements while all other measurements come from the field and inshore patch reefs. Katie Lohr measured the linear extension and calcification of the corals in a CRF nursery and is the main driver of why these corals are classified as ‘Both’.
| genotype | datafile_name | location_name |
|---|---|---|
| K1 | Paradis2019 | Auburn Lab |
| K1 | LohrPatterson2017 | CRF Tavenier Nursery |
| K2 | LohrPatterson2017 | CRF Tavenier Nursery |
| K2 | Lohr2020 | U4 Patch |
| K2 | Lohr2020 | U14 Patch |
| K3 | LohrPatterson2017 | CRF Tavenier Nursery |
| K3 | Lohr2020 | U4 Patch |
| U41 | LohrPatterson2017 | CRF Tavenier Nursery |
| U41 | Lohr2020 | U4 Patch |
| U41 | Lohr2020 | U14 Patch |
| U44 | LohrPatterson2017 | CRF Tavenier Nursery |
| U44 | Lohr2020 | U4 Patch |
| U47 | LohrPatterson2017 | CRF Tavenier Nursery |
| U73 | LohrPatterson2017 | CRF Tavenier Nursery |
| U77 | LohrPatterson2017 | CRF Tavenier Nursery |
| U77 | Lohr2020 | U4 Patch |
| U77 | Lohr2020 | U14 Patch |
| U78 | LohrPatterson2017 | CRF Tavenier Nursery |
This leads me to believe that the composite growth index is not sensitive to data comprised only of calcification or linear extension metrics, rather, the index is sensitive to evenness of sampling effort where a few high growth values in a single metric may skew the composite score. While this dampens the robustness of our index as it stands today, the index will become more robust over time with the inclusion of more datasets from the lab and field.
To support this conclusion, I am recalculating the composite growth index. However, for this index, the calcification data for Katie Lohr’s work is removed. This calcification data was obtained by collecting the buoyant weight of corals grown in a coral nursery and dominates the buoyant weight metrics as all other buoyant weight growth measured corals grown in a lab where growth rates are typically much less than that of a nursery. Thus, these genotypes will now only be classified as linear extension. I am then recreating the exact plot and tables from above on this data subset.| contrast | estimate | conf.low | conf.high | adj.p.value |
|---|---|---|---|---|
| G-Both | -0.106 | -0.634 | 0.422 | 0.882 |
| LE-Both | -0.030 | -0.296 | 0.236 | 0.960 |
| LE-G | 0.076 | -0.402 | 0.554 | 0.925 |
We can then compare the new index rankings with the old index rankings after the removal of Lohr (2017). We can see these few data points heavily weighed these genotypes.
| genotype | score.old | metrics.old | type.old | score.new | metrics.new | type.new |
|---|---|---|---|---|---|---|
| U73 | 1.658 | 5 | Both | 1.027 | 3 | LE |
| U47 | 1.587 | 5 | Both | 0.982 | 3 | LE |
| K2 | 1.536 | 7 | Both | 0.229 | 5 | LE |
| K3 | 1.530 | 7 | Both | 0.269 | 5 | LE |
| U78 | 1.515 | 5 | Both | 0.836 | 3 | LE |
| U41 | 1.455 | 7 | Both | 0.528 | 5 | LE |
| U77 | 1.210 | 7 | Both | 0.435 | 5 | LE |
| K1 | 1.072 | 5 | Both | 0.382 | 5 | Both |
| U44 | 0.765 | 7 | Both | 0.195 | 5 | LE |
In conclusion, I believe the composite growth index can align the datasets and metrics within AcDC to best describe relative performance. While the index is not without its flaws, the robustness will only increase over time with the inclusion of more traits and datasets. By using the temporal, experimental, and location filters, one can further increase the robustness of the index. For instance, one can remove lab or field data using the filters to achieve the filtering of the Lohr (2017) calcification data.
To compare these rankings to individually derived metrics, please check out the other report.